After putting some more thought into it:
Batman 1: The Black Mask, Hugo Strange and Clayface. The Black Mask and Clayface should both be defeated in this movie. Hugo Strange should stick around.
Batman 2: Court of Owls. They should be subtly hinted at in the first movie, but never shown. Having a massive secret organization as the enemy in the first movie would seem too similar to Batman Begins.
Batman 3: The Joker with Harley Quinn. Introduce Jason Todd as Robin.
Batman 4: The Joker breaks out of Akham. Cue "A Death in the Family".